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dc.contributor.authorUmeton, Renato
dc.date.accessioned2012-04-24T20:04:50Z
dc.date.available2012-04-24T20:04:50Z
dc.date.issued2012-03
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/1721.1/70121
dc.descriptionFrom Eighth Annual Meeting of the Italian Society of Bioinformatics (BITS) Pisa, Italy. 20-22 June 2011en_US
dc.description.abstractBackground The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. In fact, such models are shared to provide the characterization of molecular processes, while biomedical ontologies detail a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Indeed, having different objectives and different abstraction levels, most of these resources "speak" different languages. Semantic web technologies are here explored as a means to address some of these problems. Methods Employing an extensible collection of interpreters, we developed OREMP (Ontology Reasoning Engine for Molecular Pathways), a system that abstracts the information from different resources and combines them together into a coherent ontology. Continuing this effort we present OREMPdb; once different pathways are fed into OREMP, species are linked to the external ontologies referred and to reactions in which they participate. Exploiting these links, the system builds species-sets, which encapsulate species that operate together. Composing all of the reactions together, the system computes all of the reaction paths from-and-to all of the species-sets. Results OREMP has been applied to the curated branch of BioModels (2011/04/15 release) which overall contains 326 models, 9244 reactions, and 5636 species. OREMPdb is the semantic dictionary created as a result, which is made of 7360 species-sets. For each one of these sets, OREMPdb links the original pathway and the link to the original paper where this information first appeared.en_US
dc.description.sponsorshipUniversità degli studi della Calabria (PhD student fellowship)en_US
dc.description.sponsorshipSingapore-MIT Alliance for Research and Technology (Program in Computational and Systems Biology)en_US
dc.description.sponsorshipUniversità di Cataniaen_US
dc.publisherBioMed Central Ltden_US
dc.relation.isversionofhttp://www.biomedcentral.com/1471-2105/13/S4/S6/abstracten_US
dc.rightsCreative Commons Attributionen_US
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_US
dc.sourceBioMed Central Ltden_US
dc.titleOREMPdb: a semantic dictionary of computational pathway modelsen_US
dc.typeArticleen_US
dc.identifier.citationUmeton, Renato, Giuseppe Nicosia, and C Forbes Dewey. “OREMPdb: a Semantic Dictionary of Computational Pathway Models.” BMC Bioinformatics 13.Suppl 4 (2012): S6. Web.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biological Engineeringen_US
dc.contributor.mitauthorDewey, C. Forbes
dc.contributor.mitauthorUmeton, Renato
dc.relation.journalBMC Bioinformaticsen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2012-03-28T11:05:44Z
dc.language.rfc3066en
dc.rights.holderet al.; licensee BioMed Central Ltd.
dspace.orderedauthorsUmeton, Renato; Nicosia, Giuseppe; Dewey, C. Forbesen_US
dc.identifier.orcidhttps://orcid.org/0000-0001-7387-3572
dspace.mitauthor.errortrue
mit.licensePUBLISHER_CCen_US
mit.metadata.statusComplete


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